Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nr3c1

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
GR_ZT20 control_liver
strain
C57BL/6J
treatment
12 wk control Diet (Research Diet, D12329)
tissue
Liver
chip antibody
GR (Santa Cruz, sc-1004X)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as previously described (Uhlenhaut et al. 2012). Briefly, 200 mg of frozen liver was minced and Dounce homogenated in 0.7 mg/mL DSG crosslinker and 1% Formaldheyde. Nuclei were isolated and chromatin sonicated to a 1-0.5 kb size by using Diagenode Bioruptor Plus. Sheared chromatin was then immunoprecipitated with specific antibodies. Libraries from ChIP DNA and chromatin input were prepared by use of KAPA Hyperprep Kit (Kapa Biosystems, KK8504), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies) and used at a final concentration of 68 nM. Adapted ligated libraries were size selected (360-610 bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science, CDF2010). Libraries concentration was estimated by Real Time PCR, with KAPA Library Quantification Kit (Kapa Biosystems, KK4873). Quality of the libraries was evaluated by use of the Agilent High Sensitivity DNA Kit (Agilent) in a 2100 Bioanalyzer (Agilent).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
47627817
Reads aligned (%)
97.3
Duplicates removed (%)
17.6
Number of peaks
3557 (qval < 1E-05)

mm9

Number of total reads
47627817
Reads aligned (%)
97.2
Duplicates removed (%)
17.8
Number of peaks
3596 (qval < 1E-05)

Base call quality data from DBCLS SRA